A novel multivariate method based on principal component analysis of pre-processed sections of chromatograms is used to characterize the complex PAH pollution patterns in sediments from Guanabara Bay, Brazil. Five distinct sources of 3- to 6-ring PAHs could be revealed. The harbour is the most contaminated site in the bay, its plume stretches in a South West to North East direction and the chemical profile indicates mainly pyrogenic sources mixed with a fraction of high-molecular-weight petrogenic PAHs. Rio São João de Meriti is the second largest source of PAHs, and introduces mainly a fraction of low-molecular-weight petrogenic PAHs from the western region of Rio de Janeiro. The sites close to the ruptured pipeline at the Duque de Caxias Refinery show a distinctive pollution pattern indicating a heavy petroleum fraction. The method also led to the identification of new potential indicator ratios also involving coeluting peaks (e.g., triphenylene and chrysene).